(Q34590458)

English

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

scientific article

In more languages

default for all languages

No label defined

No description defined

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly (English)

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

whole genome sequencing

1 reference

based on heuristic

inferred from title

15

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Pieter Wesseling

12

object named as

Pieter Wesseling

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

2

object named as

Daoud Sie

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Jaap C Reijneveld

11

object named as

Jaap C Reijneveld

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

10

object named as

Gerrit A Meijer

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

author name string

Ilari Scheinin

1

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Henrik Bengtsson

3

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Mark A van de Wiel

4

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Adam B Olshen

5

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Hinke F van Thuijl

6

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Hendrik F van Essen

7

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Paul P Eijk

8

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

François Rustenburg

9

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Daniel Pinkel

13

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Donna G Albertson

14

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

language of work or name

1 reference

based on heuristic

inferred from title

publication date

18 September 2014

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Genome Research

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

24

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

12

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

2022-2032

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

ENCODE data in the UCSC Genome Browser: year 5 update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

An integrated map of genetic variation from 1,092 human genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Genetics and pharmacogenomics of diffuse gliomas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

An integrated encyclopedia of DNA elements in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Statistical challenges associated with detecting copy number variations with next-generation sequencing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Summarizing and correcting the GC content bias in high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Fast computation and applications of genome mappability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Genomic aberrations in pediatric diffuse intrinsic pontine gliomas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Chipster: user-friendly analysis software for microarray and other high-throughput data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Hallmarks of Cancer: The Next Generation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

The European Nucleotide Archive

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Preprocessing and downstream analysis of microarray DNA copy number profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

De novo assembly of human genomes with massively parallel short read sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

The Sequence Alignment/Map format and SAMtools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Fast and accurate short read alignment with Burrows-Wheeler transform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

High-resolution mapping of copy-number alterations with massively parallel sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

The fine-scale and complex architecture of human copy-number variation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Tissue preparation: Tissue issues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

A faster circular binary segmentation algorithm for the analysis of array CGH data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Structural variation in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Bioconductor: open software development for computational biology and bioinformatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

The human genome browser at UCSC

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Assembly of microarrays for genome-wide measurement of DNA copy number

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

CGHcall: calling aberrations for array CGH tumor profiles.

1 reference

https://api.crossref.org/works/10.1101%2FGR.175141.114

21 January 2018

Smoothing waves in array CGH tumor profiles

1 reference

https://api.crossref.org/works/10.1101%2FGR.175141.114

21 January 2018

Pathology databanking and biobanking in The Netherlands, a central role for PALGA, the nationwide histopathology and cytopathology data network and archive.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

27 October 2018

Detection limits of DNA copy number alterations in heterogeneous cell populations

1 reference

https://pubmed.ncbi.nlm.nih.gov/25236618

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray

1 reference

https://pubmed.ncbi.nlm.nih.gov/25236618

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/GR.175141.114

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q34590458&oldid=2086946984"